[Bioperl-l] PDB ATOM records: name, segid, etc.

[Kris Boulez]

Quoting Joe Krahn (krahn@niehs.nih.gov):
> Andrew Dalke wrote:

[ ... ]

> I think 2.1 has SEGID documented. I assumed you left it out of the
> current version because later documents declared it obsolete.
> But, we crystallographers would like it re-instated.
> 
I'm more then happy to put it in.

> All of the formats are documented here:
> http://www.rcsb.org/pdb/info.html#File_Formats_and_Standards
> 
Yes, but I can't find the 1.x format descriptions from there. I already
got it from the package from Andrew.

> <snip>
> 
> > 
> > Another place to look for details on these formats is Babel/OpenBabel
> >   http://openbabel.sourceforge.net/
> Could we just use Babel as a proxy for various formats, or do we want to
> avoid executable proxies?
> 
I started writing Bio::Structure as a way to manipulate structure based
data in BioPerl. The PDB format is the only format we (and most other
people apparently) use, so this is the only parser which is there. I
don't want to duplicate work that has already been done. 
If we want to convert one format in another I think we should interface
with OpenBabel.

Does anyone know if OpenBabel is more then a converter (i.e. could we
use to read data in and let it create Structure objects) ?

> A related issue, what do you think about incorporating bond, angle, etc.
> data, and forcefield parameters?  And things like non-bonded
> interaction analysis, H-bond detection, etc? We have various bits of
> Perl code that we are trying to organize, and BioPerl's PDB module
> would be a good place to put it.
> 
I think Bio::Structure is certainly the place these belong under. Which
data/analysis are you exactly thinking about ?


Kris,